Re: [gmx-users] radial densities

Can't think of a current program that does this. One option is to: 1. Use g_sdf from here: http://www.gromacs.org/pipermail/gmx-developers/2006-August/001786.html 1b. With the bug fix from here: http://www.gromacs.org/pipermail/gmx-developers/2006-August/001791.html BUG: line 216 of 298 should

Re: [gmx-users] Possible Bug GROMACS 3.3.1 - NMA

Yes, I'm using Cut-off. And the Error is reproducable. I'll post the bug report. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551

[gmx-users] trjconv for hexa-meric protein

Hi I simulate a hexa-meric protein (443*6=2658 residues with about 9 water) Especially, I'm interested in water behavior around the protein. The 1ns simulation is finished normally, but trjconv produces abnormal structure. For example, the protein go outside my waterbox, water molecules are

[gmx-users] change number of processors after tpbconv

hi all// is it possible to change the number of processors (mpi) when i try to continue a crashed/stopped run with tpbconv? cheers// carsten ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] change number of processors after tpbconv

Carsten Baldauf wrote: hi all// is it possible to change the number of processors (mpi) when i try to continue a crashed/stopped run with tpbconv? cheers// carsten ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] OPLS + ffgmx

Hi Mark and Chris, Thanks a lot to both of you for going through my query, for suggesting the positive and negative points of this procedure. I will think and then decide how to go about it. I am really thankful to Chris for the detailed suggestion regarding the procedure. I will come back to

Re: [gmx-users] change number of processors after tpbconv

thank you// David van der Spoel wrote: Carsten Baldauf wrote: hi all// is it possible to change the number of processors (mpi) when i try to continue a crashed/stopped run with tpbconv? cheers// carsten ___ gmx-users mailing list